One year's study of dynamic and evolution of types I and II PRRSV in a swine farm

Prevalence and genetic evolution of porcine reproductive and respiratory syndrome virus in commercial fattening pig farms in China

BACKGROUND

To investigate the prevalence and evolution of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) at commercial fattening pig farms, a total of 1397 clinical samples were collected from a single fattening cycle at seven pig farms in five provinces of China from 2020 to 2021.

RESULTS

The RT‒PCR results revealed that PRRSV was present on all seven farms, and the percentage of PRRSV-positive individuals was 17.54-53.33%. A total of 344 partial NSP2 gene sequences and 334 complete ORF5 gene sequences were obtained from the positive samples. The statistical results showed that PRRSV-2 was present on all seven commercial fattening farms, and PRRSV-1 was present on only one commercial fattening farm. A total of six PRRSV-2 subtypes were detected, and five of the seven farms had two or more PRRSV-2 subtypes. L1.8 (L1C) PRRSV was the dominant epidemic strain on five of the seven pig farms. Sequence analysis of L1.8 (L1C) PRRSV from different commercial fattening pig farms revealed that its consistency across farms varied substantially. The amino acid alignment results demonstrated that there were 131 aa discontinuous deletions in NSP2 between different L1.8 (L1C) PRRSV strains and that the GP5 mutation in L1.8 (L1C) PRRSV was mainly concentrated in the peptide signal region and T-cell epitopes. Selection pressure analysis of GP5 revealed that the use of the PRRSV MLV vaccine had no significant episodic diversifying effect on L1.8 (L1C) PRRSV.

CONCLUSION

PRRSV infection is common at commercial fattening pig farms in China, and the percentage of positive individuals is high. There are multiple PRRSV subtypes of infection at commercial fattening pig farms in China. L1.8 (L1C) is the main circulating PRRSV strain on commercial fattening pig farms. L1.8 (L1C) PRRSV detected at different commercial fattening pig farms exhibited substantial differences in consistency but similar molecular characteristics. The pressure on the GP5 of L1.8 (L1C) PRRSV may not be directly related to the use of the vaccines.

Codon Pair Deoptimization (CPD)-Attenuated PRRSV-1 Vaccination Exhibit Immunity to Virulent PRRSV Challenge in Pigs

Commercially used porcine respiratory and reproductive syndrome (PRRS) modified live virus (MLV) vaccines provide limited protection with heterologous viruses, can revert back to a virulent form and they tend to recombine with circulating wild-type strains. Codon pair deoptimization (CPD) is an advanced method to attenuate a virus that overcomes the disadvantages of MLV vaccines and is effective in various virus vaccine models. The CPD vaccine against PRRSV-2 was successfully tested in our previous study. The co-existence of PRRSV-1 and -2 in the same herd demands protective immunity against both viruses. In this study, live attenuated PRRSV-1 was constructed by recoding 22 base pairs in the ORF7 gene of the E38 strain. The efficacy and safety of the CPD live attenuated vaccine E38-ORF7 CPD to protect against virulent PRRSV-1 were evaluated. Viral load, and respiratory and lung lesion scores were significantly reduced in animals vaccinated with E38-ORF7 CPD. Vaccinated animals were seropositive by 14 days post-vaccination with an increased level of interferon-γ secreting cells. In conclusion, the codon-pair-deoptimized vaccine was easily attenuated and displayed protective immunity against virulent heterologous PRRSV-1.

Epidemiological investigation and genetic evolutionary analysis of PRRSV-1 on a pig farm in China

Porcine reproductive and respiratory syndrome virus (PRRSV) has brought serious economic losses to pig industry. PRRSV-1 have existed in China for more than 25 years. The prevalence and features of PRRSV-1 on Chinese farms are unclear. We continuously monitored PRRSV in a pig farm with strict biosafety measures in Henan Province, China, in 2020. The results showed that multiple types of PRRSV coexisted on this single pig farm. PRRSV-1 was one of the main circulating strains on the farm and was responsible for infections throughout nearly the entire epidemic cycle. Phylogenetic analysis showed that PRRSV-1 isolates from this pig farm formed an independent branch, with all isolates belonging to BJEU06-1-like PRRSV. The analysis of selection pressure on ORF5 on this branch identified 5 amino acids as positive selection sites, indicating that PRRSV-1 had undergone adaptive evolution on this farm. According to the analysis of ORF5 of PRRSV-1 on this farm, the evolutionary rate of the BJEU06-1-like branch was estimated to be 1.01 × 10^-2 substitutions/site/year. To further understand the genome-wide characteristics of PRRSV-1 on this pig farm, two full-length PRRSV-1 genomes representative of pig farms were obtained. The results of amino acid alignment revealed that although one NSP2 deletion was consistent with BJEU06-1, different new features were found in ORF3 and ORF4. According to the above results, PRRSV-1 has undergone considerable evolution in China. This study is the first to report the prevalence and characteristics of PRRSV-1 on a large farm in mainland China, which will provide a reference for the identification and further prevention and control of PRRSV-1.

Long-Term Genome Monitoring Retraces the Evolution of Novel Emerging Porcine Reproductive and Respiratory Syndrome Viruses

Porcine reproductive and respiratory syndrome virus (PRRSV) causes tremendous economic losses to the swine industry worldwide. In China, novel PRRSVs have frequently emerged in recent years, but the evolutionary relationship among these viruses has remained unclear. In the present study, a 4-year PRRSV genome-monitoring study was performed on samples from a pig farm. We observed that NADC30-like PRRSVs with higher mutation rates replaced HP-PRRSVs as the epidemic strains. We monitored the variation in the same PRRSV strain evolved in a pig herd over 2 years and observed that the low genomic similarity of NADC30-like PRRSVs results from rapid mutation. We also showed that recombination events between NADC30-like and QYYZ-like PRRSVs resulted in the complex recombination patterns of PRRSVs, which have formed gradually over time. Furthermore, recombination of the same strain can occur at different locations and increase the diversity of recombination events. Overall, these findings interpret the evolutionary patterns of novel and emerging PRRSVs, information that is crucial for PRRSV control.

Immune response and protective efficacy of intramuscular and intradermal vaccination with porcine reproductive and respiratory syndrome virus 1 (PRRSV-1) modified live vaccine against highly pathogenic PRRSV-2 (HP-PRRSV-2) challenge, either alone or in combination with of PRRSV-1

The study was conducted to evaluate the immune response of pigs vaccinated intramuscularly (IM) or intradermally (ID) with porcine reproductive and respiratory syndrome virus 1 (PRRSV-1) modified live vaccine (MLV). The protective efficacy was evaluated upon challenge with highly pathogenic (HP)-PRRSV-2, either alone or in combination with PRRSV-1. Forty-two, castrated male, PRRSV-free pigs were randomly allocated into 7 groups of 6 pig each. IM/HPPRRSV2, IM/CoChallenge, ID/HPPRRSV2 and ID/CoChallenge groups were vaccinated IM or ID with PRRSV-1 MLV (UNISTRAIN® PRRS, Laboratorios Hipra S.A., Amer, Spain) in accordance to the manufacturer's directions. NV/HPPRRSV2 and NoVac/CoChallenge groups were nonvaccinated/challenged controls. NoVac/NoChallenge group was left as the control. Antibody response, IFN-γ-secreting cells (IFN-γ-SC) and IL-10 production were evaluated following vaccination. At 35 days post vaccination (DPV), all challenged groups were intranasally inoculated with HP-PRRSV-2, either alone or in combination with PRRSV-1. PRRSV viremia and lung lesion scores were evaluated following challenge. The results demonstrated that ID vaccinated pigs had significantly lower IL-10 levels and higher IFN-γ-SC than that of IM vaccinated pigs. Following challenge with HP-PRRSV-2 either alone or with PRRSV-1, PRRSV viremia and lung lesions, both macroscopically and microscopically, were significantly reduced in vaccinated pigs than that of nonvaccinated pigs, regardless to the route of vaccine administration. ID vaccinated pigs had significantly lower levels of PRRSV viremia and lung lesion scores than that of IM vaccinated pigs. The results of the study suggested that the administration of PRRSV-1 MLV, either IM or ID, provided partial protection against HP-PRRSV-2, either alone or when cochallenged with PRRSV-1, as demonstrated by the reduction in lung lesions and viremia. The ID route might represent an alternative to improve vaccine efficacy, as it resulted in lower IL-10 levels and higher IFN-γ-SC levels.

Cell-mediated immune response and protective efficacy of porcine reproductive and respiratory syndrome virus modified-live vaccines against co-challenge with PRRSV-1 and PRRSV-2

Cell-mediated immunity (CMI), IL-10, and the protective efficacy of modified-live porcine reproductive and respiratory syndrome virus (PRRSV) vaccines (MLV) against co-challenge with PRRSV-1 and PRRSV-2 (HP-PRRSV) were investigated. Seventy, PRRSV-free, 3-week old, pigs were allocated into 7 groups. Six groups were intramuscularly vaccinated with MLV, including Porcilis (PRRSV-1 MLV, MSD Animal Health, The Netherlands), Amervac (PRRSV-1 MLV, Laboratorios Hipra, Spain), Fostera (PRRSV-2 MLV, Zoetis, USA), Ingelvac PRRS MLV and Ingelvac PRRS ATP (PRRSV-2, Boehringer Ingelheim, USA), and Prime Pac PRRS (PRRSV-2 MLV, MSD Animal Health, The Netherlands). Unvaccinated pigs were left as control. Lymphocyte proliferative response, IL-10 and IFN-γ production were determined. At 35 days post-vaccination (DPV), all pigs were inoculated intranasally with 2 ml of each PRRSV-1 (10^5.4 TCID₅₀/ml) and PRRSV-2 (10^5.2 TCID₅₀/ml, HP-PRRSV). Following challenge, sera were quantitatively assayed for PRRSV RNA. Pigs were necropsied at 7 days post-challenge. Viremia, macro- and microscopic lung lesion together with PRRSV antigen presence were evaluated in lung tissues. The results demonstrated that, regardless of vaccine genotype, CMI induced by all MLVs was relatively slow. Increased production of IL-10 in all vaccinated groups was observed at 7 and 14 DPV. Pigs in Amervac, Ingelvac MLV and Ingelvac ATP groups had significantly higher levels of IL-10 compared to Porcilis, Fostera and Prime Pac groups at 7 and 14 DPV. Following challenge, regardless to vaccine genotype, vaccinated pigs had significantly lower lung lesion scores and PRRSV antigens than those in the control group. Both PRRSV-1 and PRRSV-2 RNA were significantly reduced. Prime Pac pigs had lowest PRRSV-1 and PRRSV-2 RNA in serum, and micro- and macroscopic lung lesion scores (p < 0.05) compared to other vaccinated groups. In conclusion, PRRSV MLVs, regardless of vaccine genotype, can reduce viremia and lung lesions following co-challenge with PRRSV-1 and PRRSV-2 (HP-PRRSV). The main difference between PRRSV MLV is the production of IL-10 following vaccination.

Spatial analysis and temporal trends of porcine reproductive and respiratory syndrome in Denmark from 2007 to 2010 based on laboratory submission data

BACKGROUND

Porcine reproductive and respiratory syndrome (PRRS) has been a cause for great concern to the Danish pig industry since it was first diagnosed in 1992. The causative agent of PRRS is an RNA virus which is divided into different genotypes. The clinical signs, as well as its morbidity and mortality, is highly variable between herds and regions. Two different genotypes of PRRS virus (PRRSV) are found in Denmark: type 1 and type 2. Approximately 40% of Danish swine herds are seropositive for one or both PRRSV types. The objective of this study was to describe the temporal trend and spatial distribution of PRRSV in Danish swine herds from 2007 to 2010, based on type-specific serological tests from the PRRS surveillance and control program in Denmark using the results stored in the information management system at the National Veterinary Institute, Technical University of Denmark (DTU Vet).

RESULTS

The average monthly seroprevalence of PRRSV type 1 was 9% (minimum of 5%; maximum of 13%) in breeding herds, and 20% (minimum of 14%; maximum of 26%) in production herds; PRRSV type 2 had an average seroprevalence of 3% (minimum of 1%; maximum of 9%) in breeding herds and of 9% (minimum of 5%; maximum of 13%) within production herds. The seroconversion rate followed a similar and consistent pattern, being higher for type 1 than for type 2 for both PRRSV types. Regarding the spatiotemporal results, the relative risk distribution maps changed over time as a consequence of the changes in PRRSV seroprevalence, suggesting a general decline in the extent of areas with higher relative risk for both type 1 and 2. Local spatial analysis results demonstrated the existence of statistically significant clusters in areas where the relative risk was higher for both herds.

CONCLUSIONS

PRRSV type 1 seroprevalence was constantly higher than for PRRSV type 2 in both herd types. Significant spatial clusters were consistently found in Denmark, suggesting that PRRSV is endemic in these areas. Furthermore, relative risk distribution maps revealed different patterns over time as a consequence of the changes in seroprevalence.

Dynamics and evolution of highly pathogenic porcine reproductive and respiratory syndrome virus following its introduction into a herd concurrently infected with both types 1 and 2

Since its first emergence in Thailand in late 2010, highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) has caused sporadic outbreaks on Thai swine farms. The objective of this study was to investigate the dynamics and evolution of PRRSV in a herd experiencing an HP-PRRSV outbreak. Following its introduction, HP-PRRSV caused severe outbreaks and subsequently established persistent infection in the herd, resulting in the emergence of a novel cluster of type 2 (North American, NA) isolates. HP-PRRSV co-existed with type 1 (European, EU) isolates without influencing their development. In contrast, HP-PRRSV influenced the evolution of the type 2 (NA) isolates by increasing diversity through the addition of a novel cluster and influencing the evolution of other viral clusters previously existing in the herd. Recombination between the endemic and emerging isolates was observed. The recombinants, however, disappeared and were not able to survive in the herd. The results of this study suggest that the introduction of HP-PRRSV to a herd results in an increased diversity of genetically related isolates and persistent HP-PRRSV infection.

ORF5-based evolutionary and epidemiological dynamics of the type 1 porcine reproductive and respiratory syndrome virus circulating in Korea

This study applied a number of advanced genetic analysis tools to investigate the evolutionary trajectories and epidemiological dynamics of Korean type 1 PRRSV based on variations in the ORF5 gene over a long-term period from 2005 to 2013. Maximum likelihood phylogenetic analysis performed on large, worldwide ORF5 sequences (n=1127) strongly suggested no further introduction of genetically novel type 1 PRRSV into Korean pig farms, with the identification of only two clusters (I and II) in circulation to date. Using a codon-based extension of the Bayesian relaxed clock model, this study was able to distinguish between synonymous and non-synonymous substitutions and demonstrated that, while the absolute rates of synonymous substitution (E[S]) were similar between clusters I and II, the absolute rate of non-synonymous substitution (E[N]) was significantly different between the clusters. Cluster I was found to have an elevated E[N]/E[S] ratio relative to cluster II on the internal branches, compared to the external branches. Additionally, many fewer sites were predicted under diversifying selection in cluster II than in cluster I. Utilizing the Bayesian skyride method and the novel Bayesian birth-death skyline plot method, this study provided insights into the epidemiological dynamics of type 1 PRRSV in Korea by revealing that each cluster experienced a unique epidemic growth and by uncovering correlations between the effective population size and effective reproductive number.

Dynamics and evolution of porcine reproductive and respiratory syndrome virus (PRRSV) ORF5 following modified live PRRSV vaccination in a PRRSV-infected herd

The objective of this study was to investigate the dynamics and evolution of porcine reproductive and respiratory syndrome virus (PRRSV) ORF5 following the use of a modified live PRRSV (MLV) vaccine. A PRRSV-positive farm with coexistence of types 1 and 2 and no history of MLV vaccination was investigated. Vaccination with a type 2 MLV (Ingelvac PRRS MLV, Boehringer Ingelheim, USA) was implemented. All sows were vaccinated at monthly intervals for two consecutive months and then every third month. Piglets were vaccinated once at 7-10 days of age and weaned to nursery facilities at 21-23 days of age. Serum samples were collected monthly before and after vaccination from four population groups, including replacement gilts and suckling, nursery and finishing pigs, and assayed by PCR. After a year of blood collection, amplified products were sequenced, resulting in 277 complete ORF5 gene sequences from 145 type 1 and 132 type 2 isolates. Prior to and following vaccination, both type 1 and type 2 PRRSV were isolated and found to coexist in an individual pig. Each genotype evolved separately without influencing the strain development of the other. Although the substitution rates of both genotypes were relatively similar, MLV vaccination appears to increase the heterogenicity of type 2 PRRSV, resulting in the emergence of three novel type 2 PRRSV clusters in the herd, including an MLV-like cluster, which disappeared within the month following whole-herd vaccination. Two additional clusters included one related to the MLV vaccine and one related to the endemic cluster of the herd.

Correlation among genetic, Euclidean, temporal, and herd ownership distances of porcine reproductive and respiratory syndrome virus strains in Quebec, Canada

BACKGROUND

Porcine reproductive and respiratory syndrome (PRRS) is a viral disease that has a major economic impact for the swine industry. Its control is mostly directed towards preventing its spread which requires a better understanding of the mechanisms of transmission of the virus between herds. The objectives of this study were to describe the genetic diversity and to assess the correlation among genetic, Euclidean and temporal distances and ownership to better understand pathways of transmission.

RESULTS

A cross-sectional study was conducted on sites located in a high density area of swine production in Quebec. Geographical coordinates (longitude/latitude), date of submission and ownership were obtained for each site. ORF5 sequencing was attempted on PRRSV positive sites. Proportion of pairwise combinations of strains having ≥98% genetic homology were analysed according to Euclidean distances and ownership. Correlations between genetic, Euclidean and temporal distances and ownership were assessed using Mantel tests on continuous and binary matrices. Sensitivity of the correlations between genetic and Euclidean as well as temporal distances was evaluated for different Euclidean and temporal distance thresholds. An ORF5 sequence was identified for 132 of the 176 (75%) PRRSV positive sites; 122 were wild-type strains. The mean (min-max) genetic, Euclidean and temporal pairwise distances were 11.6% (0-18.7), 15.0 km (0.04-45.7) and 218 days (0-852), respectively. Significant positive correlations were observed between genetic and ownership, genetic and Euclidean and between genetic and temporal binary distances. The relationship between genetic and ownership suggests either common sources of animals or semen, employees, technical services or vehicles, whereas that between genetic and Euclidean binary distances is compatible with area spread of the virus. The latter correlation was observed only up to 5 km.

CONCLUSIONS

This study suggests that transmission of PRRSV is likely to occur between sites belonging to the same owner or through area spread within a 5 km distance. Both should be considered in the perspective of prevention.